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[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Richard Zander Richard.Zander at mobot.org
Tue Jul 14 09:40:33 CDT 2015


This thread seems to consider classification either as a non-theoretic pattern of evidence or a subjective art form. I think that there are objective, scientific criteria for judging a "best" classification, e.g. the dissilient species/genus/family concept in:
http://www.mobot.org/plantscience/ResBot/Repr/Zander-Framework.pdf 

Stephen suggests that " The term "natural classification" refers to a classification based on evolutionary/phylogenetic relationships"
Which is it? Phylogenetic relationships minimize paraphyly, evolutionary relationships maximize paraphyly. The classifications are commonly different.

-------
Richard H. Zander
Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA
richard.zander at mobot.org 
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/ 


-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Jensen
Sent: Tuesday, July 14, 2015 8:46 AM
To: Stephen Thorpe
Cc: Taxacom
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Stephen,

Isn't ant classification simply one of a set of alternative classifications?

And, you have your interpretation of what a "natural" classification is, but this is not something that has been accepted by all.  The history of the concept of natural classification is fraught with disagreements, sometimes quite heated, about this idea.


Cheers,

Dick J

On Mon, Jul 13, 2015 at 5:30 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:

> Not that well said, actually! The term "natural classification" refers 
> to a classification based on evolutionary/phylogenetic relationships 
> rather than on subjective judgements of similarity and/or "groups of convenience".
> As I said earlier in this thread, one is free to choose a 
> classification, and that of Ruggiero et al. is a choice one may 
> choose, but there could be problems resulting from sticking too 
> rigidly to it for too long, that's all. There may be better 
> alternatives. I would really hate to see it adopted as some kind of 
> "official standard", when all it is is one suggestion.
>
> Stephen
>
>
> --------------------------------------------
> On Tue, 14/7/15, Robin Leech <releech at telus.net> wrote:
>
>  Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level 
> Classification of All Living Organisms"
>  To: "'Pierre Deleporte'" <pierre.deleporte at univ-rennes1.fr>,
> taxacom at mailman.nhm.ku.edu
>  Received: Tuesday, 14 July, 2015, 9:16 AM
>
>  Well said, Pierre.
>  Robin
>
>  -----Original Message-----
>  From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
>  On Behalf Of Pierre Deleporte
>  Sent: July-13-15 2:16 PM
>  To: taxacom at mailman.nhm.ku.edu
>  Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher  Level 
> Classification of All Living Organisms"
>
>
>  all classifications are concepts - there is no  classification 
> without a classifier - there is no "natural"
>  classification standing in itself out there in the natural  wild 
> (proponents of "natural" classifications should  meticulously explain 
> what they mean)
>
>  useful classifications serve communication purposes (talking  of 
> things or 'objects'  by meaningful classes rather  than on by
>  one)
>
>  many classifications can be useful, provided that they fit  their 
> goals (what kind of information do we want to convey
>  ?) and their specification (what are the desired properties  of such 
> a classification, given its goals ?)
>
>  in the present case, the classification of Ruggiero et al.
>  should be evaluated according to its specific goals (some  kind of 
> informal "majority rule consensus" for practical  purposes of 
> stability on a 5-years basis)
>
>  criticisms in terms of "scientificity" or "naturalness" are  largely 
> missing the point
>
>  Best,
>  Pierre
>
>
>
>  Le 13/07/2015 19:45, Richard Pyle wrote :
>  > Hi Stephen,
>  >
>  > A piece of string is as long as it needs to be to  perform a 
> specified task.
>  > In this case, you still seem to be having trouble  understanding 
> what  > the specific task of the CoL consensus taxonomy  is.  Tony 
> Rees  > answered much more effectively than I could have; but  the key 
> point to  > understand is that a consensus taxonomy of this sort is  
> established  > explicitly to facilitate harmony among disparate  
> datasets, to more  > effectively allow cross-dataset comparisons, and 
> to  dramatically  > simplify activities that benefit from a general  
> organization of  > biological names into a rough/approximate SHARED  
> classification.  In  > this context, the importance of stability and 
> shared  use of the  > consensus classification across multiple 
> data-providing  constituents  > VASTLY exceeds the importance of 
> reflecting the  evolutionary  > speculation du jour.  We have plenty 
> of  information streams to provide  > dynamic/evolutionary 
> classifications as new information  becomes  > available in real time.  
> What we've been lacking  (prior to the  > establishment of this CoL 
> consensus taxonomy), is a  community-oriented classification 
> "flag-pole" around which  data content providers can collectively 
> rally.
>  >
>  > Also, your reference to a "new species" further reveals  your  > 
> misunderstanding of what this consensus classification  is intended  > 
> for. If you had read the paper, and downloaded the  classification, 
> you  > would see that it only goes down as far as the rank of  Order.  
> More  > granular changes to taxonomy (e.g., families, genera,  
> species, etc.)  > are not included (those are in the realm of the  
> much-more dynamically updated CoL itself).
>  > Personally, I think a consensus classification at the  rank of 
> Order  > and higher probably does not need to be updated more  than 
> once a  > decade, but I suppose that revisiting it every five  years 
> is a reasonable frequency.
>  >
>  > In any case, I agree with Tony that the discussion has  gotten a 
> bit  > off track.
>  >
>  > Aloha,
>  > Rich
>  >
>  > Richard L. Pyle, PhD
>  > Database Coordinator for Natural Sciences | Associate  Zoologist in  
> > Ichthyology | Dive Safety Officer Department of Natural  Sciences,  
> > Bishop Museum, 1525 Bernice St., Honolulu, HI 96817  > Ph: 
> (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org
>
>  > http://hbs.bishopmuseum.org/staff/pylerichard.html
>  >
>  >
>  >
>  >> -----Original Message-----
>  >> From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
>  >> Sent: Sunday, July 12, 2015 10:40 AM  >> To: Richard Jensen  >> 
> Cc: Kenneth Kinman; Taxacom; Richard Pyle  >> Subject: Re: [Taxacom] 
> New paper: Ruggiero et al.
>  "A Higher Level
>  >> Classification of All Living Organisms"
>  >>
>  >> Dick,
>  >> Yes, but how long is a piece of string? Five years  is too long!
>  >> Problems
>  > arise
>  >> trying to fit new species into classifications  which don't yet  
> >> recognise  > the  >> relevant higher taxa. Do we really want a 5 
> year  time lag for new  > species??
>  >> Stephen
>  >>
>  >> --------------------------------------------
>  >> On Mon, 13/7/15, Richard Jensen <rjensen at saintmarys.edu>
>  wrote:
>  >>
>  >>   Subject: Re: [Taxacom] New paper:
>  Ruggiero et al. "A Higher Level
>  >> Classification of All Living Organisms"
>  >>   To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
>  >>   Cc: "Kenneth Kinman" <kinman at hotmail.com>,
>  "Taxacom"
>  >> <taxacom at mailman.nhm.ku.edu>,
>  "Richard Pyle"
>  >> <deepreef at bishopmuseum.org>
>  >>   Received: Monday, 13 July, 2015,
>  4:30 AM
>  >>
>  >>   Stephen,
>  >>   I didn't miss your point.
>  Anyone who works  in
>  >> taxonomy/systematics is
>  > well
>  >> aware of the lag time  between a taxonomist  making a discovery 
> and  >> the  > rest  >> of us  learning about it.  Thus, all  
> classifications are  restricted  >> to  > what is  >> presently known 
> by those constructing  the  classification - they  >> cannot be 
> expected to add caveats  or make  allowances for information  >> that, 
> while  > just  >> discovered a nanosecond before they submitted their  
> final  edited  >> copy,  > was  >> not available to them.
>  >>   Let's be realistic about this.
>  >>   Cheers,
>  >>   Dick J
>  >>   On Sat, Jul 11, 2015
>  >>   at 6:26 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
>  >>   wrote:
>  >>   Dick
>  >>   J said: ..., perhaps I missed
>  something in Stephen's  last note;
>  >> isn't
>  > any
>  >> classification (except for those  that are  purely fanciful) 
> limited  >> by  > what is  >> presently  known?
>  >>
>  >>
>  >>
>  >>   Yes, you did miss something, i.e.
>  the point! My point was  that
>  > classification
>  >> (particularly when based on phylogenetic
>  >>   analyses) is continuously changing
>  with new information  coming in
>  >> all
>  > the
>  >> time. Yet, I strongly suspect that it may  be  something like at 
> least  >> a  > decade  >> before CoL, etc. think  about reviewing the  
> results of Ruggiero et al.
>  > (2015).
>  >>
>  >>
>  >>   Stephen
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>   --------------------------------------------
>  >>
>  >>   On Sun, 12/7/15, Richard Jensen
>  <rjensen at saintmarys.edu>
>  >>   wrote:
>  >>
>  >>
>  >>
>  >>    Subject: Re: [Taxacom] New paper:
>  Ruggiero et al. "A  Higher Level
>  >> Classification of All Living Organisms"
>  >>
>  >>    To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
>  >>
>  >>    Cc: "Kenneth Kinman" <kinman at hotmail.com>,
>  "Taxacom"
>  >> <taxacom at mailman.nhm.ku.edu>,
>  deepreef at bishopmuseum.org
>  >>
>  >>    Received: Sunday, 12 July, 2015, 1:57
>  AM
>  >>
>  >>
>  >>
>  >>    Hi
>  >>
>  >>    all,
>  >>
>  >>    A couple of
>  >>
>  >>    observations:
>  >>
>  >>    First,
>  >>
>  >>    as Richard Pyle noted, consensus does
>  not necessarily  mean
>  >>
>  >>    unanimity.  If so, then most
>  political bills would never  be
>  >>
>  >>    passed.  Think of 'consensus
>  trees"; these  reflect
>  >>
>  >>    areas of agreement among competing
>  views and leave the
>  >>
>  >>    differences largely unresolved.
>  >>
>  >>    Second, perhaps I missed something
>  >>
>  >>    in Stephen's last note; isn't any
>  classification
>  >>
>  >>    (except for those that are purely
>  fanciful) limited by  what
>  >>
>  >>    is presently known?
>  >>
>  >>    Third, I haven't read the paper,
>  >>
>  >>    but comments made by several
>  participants certainly come
>  >>
>  >>    close to reflecting the thinking of
>  numerical  taxonomists,
>  >>
>  >>    whose classifications were based on
>  overall patterns of
>  >>
>  >>    agreement among all characters
>  available (or all  characters
>  >>
>  >>    used in the particular
>  analysis).  These classifications
>  >>
>  >>    were intended, in keeping with ideas
>  expressed by  Gilmour,
>  >>
>  >>    to be useful and, perhaps, serve as
>  the basis for  inferring
>  >>
>  >>    components of evolutionary
>  relationships (although this  was
>  >>
>  >>    not the goal). Based on what I've read
>  here, the new
>  >>
>  >>    classification attempts to provide a
>  useful
>  >>
>  >>    consensus.
>  >>
>  >>    Cheers,
>  >>
>  >>    Dick J
>  >>
>  >>    On Fri, Jul 10, 2015 at
>  >>
>  >>    11:14 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
>  >>
>  >>    wrote:
>  >>
>  >>    I have no
>  >>
>  >>    problem with alphabetical sequencing
>  of taxa at each  level,
>  >>
>  >>    in fact I prefer it. My only gripe is
>  that the paper be  seen
>  >>
>  >>    for what it really is, i.e. simply a
>  choice of
>  >>
>  >>    classification, based in part on
>  PRESENTLY available
>  >>
>  >>    evidence. Also, classifications should
>  really be  specified
>  >>
>  >>    from the bottom up. Top down
>  approaches just push a lot  of
>  >>
>  >>    unresolved rubbish down to the lower
>  levels and ignore
>  >>
>  >>    it.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>    Stephen
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  --------------------------------------------
>  >>
>  >>
>  >>
>  >>    On Sat, 11/7/15, Richard Pyle <deepreef at bishopmuseum.org>
>  >>
>  >>    wrote:
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Subject: Re: [Taxacom] New
>  paper: Ruggiero et al.
>  >>   "A
>  >>
>  >>    Higher Level
>  Classification of All Living
>  >>
>  >>    Organisms"
>  >>
>  >>
>  >>
>  >>     To: "'Kenneth Kinman'"
>  <kinman at hotmail.com>,
>  >>
>  >>    taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     Received: Saturday, 11
>  July, 2015, 2:37 PM
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Sure, one could argue
>  >>
>  >>
>  >>
>  >>     indefinitely about how to
>  contruct a "better"
>  >>
>  >>
>  >>
>  >>     consensus
>  classification.  But these LITERALLY
>  >>
>  >>
>  >>
>  >>     endless arguments are
>  exactly
>  >>
>  >>
>  >>
>  >>     why no such
>  >>
>  >>
>  >>
>  >>     comprehensive
>  classification has previously been
>  >>
>  >>    presented
>  >>
>  >>
>  >>
>  >>     FOR
>  >>
>  >>
>  >>
>  >>     THE PURPOSES INTENDED BY
>  THIS
>  >>
>  >>
>  >>
>  >>     classification.  The
>  value of this listing is
>  >>
>  >>
>  >>
>  >>     not the "classification"
>  part, so
>  >>
>  >>
>  >>
>  >>     much as it is the
>  "consensus" part.
>  >>
>  >>
>  >>
>  >>     Consensus is not the same
>  thing as unanimity.
>  >>
>  >>
>  >>
>  >>     You can certainly convey
>  your
>  >>
>  >>
>  >>
>  >>     personal
>  >>
>  >>
>  >>
>  >>     opinions (as listed below)
>  to the architects of the
>  >>
>  >>    list,
>  >>
>  >>
>  >>
>  >>     and maybe
>  >>
>  >>
>  >>
>  >>     a future version will be
>  altered
>  >>
>  >>
>  >>
>  >>     to reflect them (assuming
>  your opinions
>  >>
>  >>
>  >>
>  >>     resonate with the broader
>  consensus).
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     In any case, sequencing of
>  names in a list is
>  >>
>  >>
>  >>
>  >>     an incredibly BAD way to
>  >>
>  >>
>  >>
>  >>     represent
>  >>
>  >>
>  >>
>  >>     phylogenetic information;
>  ESPECIALLY in the context of
>  >>
>  >>    that
>  >>
>  >>
>  >>
>  >>     this
>  >>
>  >>
>  >>
>  >>     particular list is intended
>  for.  If
>  >>
>  >>
>  >>
>  >>     you want to represent
>  affinities of
>  >>
>  >>
>  >>
>  >>     taxa,
>  >>
>  >>
>  >>
>  >>     there are three basic ways
>  to do it:
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     1)      Come
>  up with a mark-up scheme (like
>  >>
>  >>
>  >>
>  >>     yours)
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     2)
>  >>
>  >>
>  >>
>  >>     Acknowledge names at ever
>  finer units of intermediate
>  >>
>  >>    ranks,
>  >>
>  >>
>  >>
>  >>     so that
>  >>
>  >>
>  >>
>  >>     relationships can be
>  represented
>  >>
>  >>
>  >>
>  >>     within nested sets
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     3)
>  >>
>  >>
>  >>
>  >>       Draw a cladogram
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     For the purposes of this
>  list,
>  >>
>  >>
>  >>
>  >>     any sequence other than
>  alphabetical
>  >>
>  >>
>  >>
>  >>     (particularly if some sort
>  of information is
>  >>
>  >>
>  >>
>  >>     intended to be conveyed by
>  the
>  >>
>  >>
>  >>
>  >>     particular
>  >>
>  >>
>  >>
>  >>     sequence) would have been a
>  very silly thing to do.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Aloha,
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Rich
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     From: Kenneth Kinman
>  [mailto:kinman at hotmail.com]
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Sent: Friday, July 10, 2015
>  3:39 PM
>  >>
>  >>
>  >>
>  >>     To: deepreef at bishopmuseum.org;
>  >>
>  >>
>  >>
>  >>     taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     Subject: RE: [Taxacom] New
>  paper: Ruggiero et
>  >>
>  >>
>  >>
>  >>     al. "A Higher Level
>  >>
>  >>
>  >>
>  >>     Classification of
>  >>
>  >>
>  >>
>  >>     All Living Organisms"
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Hi Rich,
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>     I think John is
>  >>
>  >>
>  >>
>  >>     being overly harsh.
>  Overall, it's not a bad
>  >>
>  >>
>  >>
>  >>     classification, but I think
>  it certainly could
>  >>
>  >>
>  >>
>  >>     be made better.  The
>  protist
>  >>
>  >>
>  >>
>  >>     classification
>  >>
>  >>
>  >>
>  >>     is very good, thanks to the
>  work of Thomas
>  >>
>  >>
>  >>
>  >>     Cavalier-Smith.
>  >>
>  >>
>  >>
>  >>     It's too bad he
>  >>
>  >>
>  >>
>  >>     couldn't get his co-authors
>  to classify
>  >>
>  >>    Posibacteria
>  >>
>  >>
>  >>
>  >>     and
>  >>
>  >>
>  >>
>  >>     Archaebacteria together in
>  one Kingdom
>  >>
>  >>
>  >>
>  >>     (and Negibacteria in
>  another).  I
>  >>
>  >>
>  >>
>  >>     still
>  >>
>  >>
>  >>
>  >>     think alphabetizing the
>  lists is still a sad loss of
>  >>
>  >>
>  >>
>  >>     information.  It
>  >>
>  >>
>  >>
>  >>     may be a bit more
>  >>
>  >>
>  >>
>  >>     convenient for some, but
>  I'm sure many others will
>  >>
>  >>
>  >>
>  >>     find
>  >>
>  >>
>  >>
>  >>     the loss of information
>  more than just
>  >>
>  >>
>  >>
>  >>     an inconvenience.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>     I don't understand why they
>  >>
>  >>
>  >>
>  >>     didn't subdivide the list
>  of orders of
>  >>
>  >>
>  >>
>  >>     eutherian mammals (and
>  splitting Pilosa and
>  >>
>  >>
>  >>
>  >>     Cingulata as separate
>  orders
>  >>
>  >>
>  >>
>  >>     unfortunately
>  >>
>  >>
>  >>
>  >>     eliminated the more
>  familiar name Xenarthra, as well as
>  >>
>  >>
>  >>
>  >>     being
>  >>
>  >>
>  >>
>  >>     separated
>  alphabetically).  And of
>  >>
>  >>
>  >>
>  >>     course, I would raise Aves
>  back to Class
>  >>
>  >>
>  >>
>  >>     status, and add an {{Aves}}
>  marker within
>  >>
>  >>
>  >>
>  >>     Reptilia.  Anyway,
>  even if they
>  >>
>  >>
>  >>
>  >>     insist on
>  >>
>  >>
>  >>
>  >>     retaining the alphabetical
>  "convention" for
>  >>
>  >>    the
>  >>
>  >>
>  >>
>  >>     convenience of
>  >>
>  >>
>  >>
>  >>     some, there is still
>  plenty
>  >>
>  >>
>  >>
>  >>     of room for improvement in
>  my opinion.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     ---------------Ken
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     P.S.  Hexapoda is
>  probably
>  >>
>  >>
>  >>
>  >>     polyphyletic.
>  Collembola almost certainly
>  >>
>  >>
>  >>
>  >>     evolved hexapody
>  independently from one group
>  >>
>  >>
>  >>
>  >>     of crustaceans, and the
>  >>
>  >>
>  >>
>  >>     insects from a
>  >>
>  >>
>  >>
>  >>     different group of
>  crustaceans
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     .
>  >>
>  >>
>  >>
>  >>
>  >
>  >
>  
> ----------------------------------------------------------------------
>  > ----
>  > --
>  >>
>  >>
>  >>
>     ---------------------------------------------
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     > From: deepreef at bishopmuseum.org
>  >>
>  >>
>  >>
>  >>     > To: calabar.john at gmail.com;
>  >>
>  >>
>  >>
>  >>     taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     > Date: Fri, 10 Jul 2015
>  14:52:03 -1000
>  >>
>  >>
>  >>
>  >>     > Subject: Re: [Taxacom]
>  New paper: Ruggiero
>  >>
>  >>
>  >>
>  >>     et al. "A Higher Level
>  >>
>  >>
>  >>
>  >>     Classification
>  >>
>  >>
>  >>
>  >>     of All Living Organisms"
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Hi John,
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > I think you would need
>  to read the full
>  >>
>  >>
>  >>
>  >>     paper (not just the two
>  lines of
>  >>
>  >>
>  >>
>  >>     text I
>  >>
>  >>
>  >>
>  >>     quoted from the abstract)
>  before you could make an
>  >>
>  >>
>  >>
>  >>     assessment as to
>  >>
>  >>
>  >>
>  >>     whether or not their work
>  >>
>  >>
>  >>
>  >>     fits within your own
>  personal definition of
>  >>
>  >>
>  >>
>  >>     "science". Considerably
>  more
>  >>
>  >>
>  >>
>  >>     investigation would be
>  required before you
>  >>
>  >>
>  >>
>  >>     could confidently infer
>  whether or not the work
>  >>
>  >>
>  >>
>  >>     falls within the authors'
>  >>
>  >>
>  >>
>  >>     own personal
>  >>
>  >>
>  >>
>  >>     definitions of "science".
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Aloha,
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Rich
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > From: John Grehan
>  [mailto:calabar.john at gmail.com]
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     > Sent: Friday, July 10,
>  2015 1:00 PM
>  >>
>  >>
>  >>
>  >>     > To: Richard Pyle;
>  taxacom
>  >>
>  >>
>  >>
>  >>     > Subject: Re: [Taxacom]
>  New paper: Ruggiero
>  >>
>  >>
>  >>
>  >>     et al. "A Higher Level
>  >>
>  >>
>  >>
>  >>     Classification
>  >>
>  >>
>  >>
>  >>     of All Living Organisms"
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Yes I was implying
>  (explicitly) that the
>  >>
>  >>
>  >>
>  >>     authors of the paper appear
>  to
>  >>
>  >>
>  >>
>  >>     have a
>  >>
>  >>
>  >>
>  >>     definition of science
>  (assuming that the classification
>  >>
>  >>    was
>  >>
>  >>
>  >>
>  >>     being
>  >>
>  >>
>  >>
>  >>     represented as science)
>  where science
>  >>
>  >>
>  >>
>  >>     is a 'consensus' of
>  opinion
>  >>
>  >>
>  >>
>  >>     compromising conflicting
>  information. When one
>  >>
>  >>
>  >>
>  >>     comes up with a compromise
>  of
>  >>
>  >>
>  >>
>  >>     the sort it
>  >>
>  >>
>  >>
>  >>     does not appear to be a
>  process that is attempting to
>  >>
>  >>
>  >>
>  >>     reflect
>  >>
>  >>
>  >>
>  >>     reality (whatever that
>  might be),
>  >>
>  >>
>  >>
>  >>     but just a compromise
>  between different
>  >>
>  >>
>  >>
>  >>     opinions. A good example of
>  this is how
>  >>
>  >>
>  >>
>  >>     so-called ecological areas
>  were
>  >>
>  >>
>  >>
>  >>     defined in
>  >>
>  >>
>  >>
>  >>     New Zealand (Under the
>  Protected Natural Areas program,
>  >>
>  >>    and
>  >>
>  >>
>  >>
>  >>     with
>  >>
>  >>
>  >>
>  >>     lots of money to boot)
>  according to
>  >>
>  >>
>  >>
>  >>     compromises over different
>  opinions
>  >>
>  >>
>  >>
>  >>     about
>  >>
>  >>
>  >>
>  >>     where the boundaries
>  between the areas were to be drawn
>  >>
>  >>
>  >>
>  >>     (said
>  >>
>  >>
>  >>
>  >>     boundaries having no
>  reality anyway,
>  >>
>  >>
>  >>
>  >>     hence the ability to
>  'compromise').
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Perhaps I am being
>  >>
>  >>
>  >>
>  >>     awfully presumptuous, but
>  if it is presumptuous to
>  >>
>  >>
>  >>
>  >>     regard consensus opinions
>  as outside science
>  >>
>  >>
>  >>
>  >>     then so be it.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > John Grehan
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > On Fri, Jul 10, 2015
>  >>
>  >>
>  >>
>  >>     at 4:06 PM, Richard Pyle
>  <deepreef at bishopmuseum.org>
>  >>
>  >>
>  >>
>  >>     wrote:
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > The "nature of
>  reality" is
>  >>
>  >>
>  >>
>  >>     sufficiently vague that it
>  could be interpreted
>  >>
>  >>
>  >>
>  >>     just as broadly as
>  "science" can
>  >>
>  >>
>  >>
>  >>     be.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > My only point is
>  >>
>  >>
>  >>
>  >>     that the outer boundaries
>  of "science" are
>  >>
>  >>    not
>  >>
>  >>
>  >>
>  >>     well
>  >>
>  >>
>  >>
>  >>     defined. Controlled
>  experimentation
>  >>
>  >>
>  >>
>  >>     following the scientific
>  method is
>  >>
>  >>
>  >>
>  >>     squarely
>  >>
>  >>
>  >>
>  >>     within the realm of
>  science, and most would argue that
>  >>
>  >>
>  >>
>  >>     things like
>  >>
>  >>
>  >>
>  >>     Astrology are pretty
>  clearly at
>  >>
>  >>
>  >>
>  >>     the very outskirts. In
>  between those is a
>  >>
>  >>
>  >>
>  >>     very broad range of
>  activities, such as
>  >>
>  >>
>  >>
>  >>     phylogenetics, taxonomy,
>  >>
>  >>
>  >>
>  >>     nomenclature,
>  >>
>  >>
>  >>
>  >>     informatics, and a whole
>  host of other things that may
>  >>
>  >>    or
>  >>
>  >>
>  >>
>  >>     may
>  >>
>  >>
>  >>
>  >>     not conform to some
>  particular
>  >>
>  >>
>  >>
>  >>     person's definition of
>  "science".
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Your comment, to
>  >>
>  >>
>  >>
>  >>     which I was responding,
>  seemed to imply that we all
>  >>
>  >>
>  >>
>  >>     (including the authors of
>  the paper) share a
>  >>
>  >>
>  >>
>  >>     definition of science that
>  >>
>  >>
>  >>
>  >>     would
>  >>
>  >>
>  >>
>  >>     unambiguously exclude their
>  paper from
>  >>
>  >>    "science"
>  >>
>  >>
>  >>
>  >>     (i.e., the notion
>  >>
>  >>
>  >>
>  >>     that the authors
>  >>
>  >>
>  >>
>  >>     self-evidently "admit" that
>  their work is not
>  >>
>  >>
>  >>
>  >>     science).
>  >>
>  >>
>  >>
>  >>     That seemed awfully
>  presumptuous
>  >>
>  >>
>  >>
>  >>     of you.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Aloha,
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Rich
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > From: John Grehan
>  >>
>  >>
>  >>
>  >>     [mailto:calabar.john at gmail.com]
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     > Sent: Friday, July 10,
>  2015 9:52 AM
>  >>
>  >>
>  >>
>  >>     > To: Richard Pyle
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Subject: Re:
>  >>
>  >>
>  >>
>  >>     [Taxacom] New paper:
>  Ruggiero et al. "A Higher
>  >>
>  >>    Level
>  >>
>  >>
>  >>
>  >>     Classification of All
>  Living Organisms"
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Perhaps, but what do
>  >>
>  >>
>  >>
>  >>     you think is incorrect
>  about the one I gave? Are you
>  >>
>  >>
>  >>
>  >>     saying consensus opinion is
>  science?
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > John Grehan
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > On Fri, Jul 10, 2015
>  >>
>  >>
>  >>
>  >>     at 3:30 PM, Richard Pyle
>  <deepreef at bishopmuseum.org>
>  >>
>  >>
>  >>
>  >>     wrote:
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > We all like to believe
>  our own definition
>  >>
>  >>
>  >>
>  >>     of "science" is the correct
>  one.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Sigh..
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Rich
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > From: John Grehan
>  >>
>  >>
>  >>
>  >>     [mailto:calabar.john at gmail.com]
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     > Sent: Friday, July 10,
>  2015 9:23 AM
>  >>
>  >>
>  >>
>  >>     > To: Richard Pyle
>  >>
>  >>
>  >>
>  >>     > Cc:
>  >>
>  >>
>  >>
>  >>     TAXACOM
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Subject: Re: [Taxacom]
>  New paper: Ruggiero
>  >>
>  >>
>  >>
>  >>     et al. "A Higher Level
>  >>
>  >>
>  >>
>  >>     Classification
>  >>
>  >>
>  >>
>  >>     of All Living Organisms"
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > At least the quotes
>  show that the authors
>  >>
>  >>
>  >>
>  >>     admit their work not be
>  science
>  >>
>  >>
>  >>
>  >>     (if science
>  >>
>  >>
>  >>
>  >>     is understood to be about
>  the nature of reality beyond
>  >>
>  >>
>  >>
>  >>     'consensus' opinion).
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > John Grehan
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > On Fri, Jul 10, 2015
>  >>
>  >>
>  >>
>  >>     at 3:07 PM, Richard Pyle
>  <deepreef at bishopmuseum.org>
>  >>
>  >>
>  >>
>  >>     wrote:
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Hmmm.... I've been
>  deliberately quiet
>  >>
>  >>
>  >>
>  >>     on this thread as well. I
>  appreciate
>  >>
>  >>
>  >>
>  >>     the
>  >>
>  >>
>  >>
>  >>     viewpoints of Ken and
>  others in terms of holophyly, the
>  >>
>  >>
>  >>
>  >>     value of
>  >>
>  >>
>  >>
>  >>     acknowledging paraphyletic
>  taxa
>  >>
>  >>
>  >>
>  >>     through Linnean
>  nomenclature, etc. This is
>  >>
>  >>
>  >>
>  >>     all good philosophical
>  grit, and I enjoy the
>  >>
>  >>
>  >>
>  >>     intellectual stimulation
>  as
>  >>
>  >>
>  >>
>  >>     much as
>  >>
>  >>
>  >>
>  >>     anyone.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > However,
>  >>
>  >>
>  >>
>  >>     this thread began (and
>  remains?) relevant to the PLoS
>  >>
>  >>    ONE
>  >>
>  >>
>  >>
>  >>     publication of Ruggiero et
>  al., which provides
>  >>
>  >>
>  >>
>  >>     a generalized **CONSENSUS
>  >>
>  >>
>  >>
>  >>     CLASSIFICATION**.
>  >>
>  >>
>  >>
>  >>     Perhaps there is some
>  misunderstanding on what is meant
>  >>
>  >>
>  >>
>  >>     by
>  >>
>  >>
>  >>
>  >>     this term (and the
>  associated
>  >>
>  >>
>  >>
>  >>     classification)? Anyone who
>  read as far as the
>  >>
>  >>
>  >>
>  >>     abstract of this paper
>  should at least know
>  >>
>  >>
>  >>
>  >>     that:
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > "This
>  >>
>  >>
>  >>
>  >>     classification is neither
>  phylogenetic nor evolutionary
>  >>
>  >>    but
>  >>
>  >>
>  >>
>  >>     instead
>  >>
>  >>
>  >>
>  >>     represents a consensus view
>  that
>  >>
>  >>
>  >>
>  >>     accommodates taxonomic
>  choices and
>  >>
>  >>
>  >>
>  >>     practical
>  >>
>  >>
>  >>
>  >>     compromises among diverse
>  expert opinions, public
>  >>
>  >>    usages,
>  >>
>  >>
>  >>
>  >>     and
>  >>
>  >>
>  >>
>  >>     conflicting evidence about
>  the
>  >>
>  >>
>  >>
>  >>     boundaries between taxa and
>  the ranks of
>  >>
>  >>
>  >>
>  >>     major taxa, including
>  kingdoms."
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > And:
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > "Beyond its
>  >>
>  >>
>  >>
>  >>     immediate use as a
>  management tool for the CoL and ITIS
>  >>
>  >>
>  >>
>  >>     (Integrated Taxonomic
>  Information System), it
>  >>
>  >>
>  >>
>  >>     is immediately valuable as
>  a
>  >>
>  >>
>  >>
>  >>     reference for
>  >>
>  >>
>  >>
>  >>     taxonomic and biodiversity
>  research, as a tool for
>  >>
>  >>
>  >>
>  >>     societal
>  >>
>  >>
>  >>
>  >>     communication, and as a
>  >>
>  >>
>  >>
>  >>     classificatory "backbone"
>  for biodiversity
>  >>
>  >>
>  >>
>  >>     databases, museum
>  collections, libraries, and
>  >>
>  >>
>  >>
>  >>     textbooks."
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     In this context, it is
>  ABSOLUTELY CORRECT that the
>  >>
>  >>    subtaxa
>  >>
>  >>
>  >>
>  >>     within a taxon
>  >>
>  >>
>  >>
>  >>     are alphabetically
>  arranged!
>  >>
>  >>
>  >>
>  >>     It is absolutely NOT
>  intended to reflect any
>  >>
>  >>
>  >>
>  >>     sort of "naturalness" in
>  patterns of
>  >>
>  >>
>  >>
>  >>     evolution. Yes, it probably
>  does kinda-
>  >>
>  >>
>  >>
>  >>     sorta- happen to reflect
>  modern views of
>  >>
>  >>
>  >>
>  >>     evolutionary relationships
>  >>
>  >>
>  >>
>  >>     (otherwise there
>  >>
>  >>
>  >>
>  >>     wouldn't be much consensus
>  behind it). But its
>  >>
>  >>    function
>  >>
>  >>
>  >>
>  >>     is
>  >>
>  >>
>  >>
>  >>     to serve as a tool for
>  informatics and
>  >>
>  >>
>  >>
>  >>     generalized (i.e., highly
>  simplified)
>  >>
>  >>
>  >>
>  >>     organizational
>  representation of life on Earth.
>  >>
>  >>
>  >>
>  >>     As such, it is
>  >>
>  >>
>  >>
>  >>     overwhelmingly valuable to
>  >>
>  >>
>  >>
>  >>     the people for whom it was
>  intended (see second
>  >>
>  >>
>  >>
>  >>     quote above).
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Aloha,
>  >>
>  >>
>  >>
>  >>     > Rich
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > > -----Original
>  Message-----
>  >>
>  >>
>  >>
>  >>     > > From: Taxacom
>  [mailto:taxacom-bounces at mailman.nhm.ku.edu]
>  >>
>  >>
>  >>
>  >>     On Behalf
>  >>
>  >>
>  >>
>  >>     > > Of Richard
>  Zander
>  >>
>  >>
>  >>
>  >>     > > Sent: Friday,
>  July 10, 2015 7:51
>  >>
>  >>
>  >>
>  >>     AM
>  >>
>  >>
>  >>
>  >>     > > To: TAXACOM
>  >>
>  >>
>  >>
>  >>     > > Subject: Re:
>  [Taxacom] New paper:
>  >>
>  >>
>  >>
>  >>     Ruggiero et al. "A Higher
>  Level
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Classification of All
>  Living Organisms"
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Maybe now
>  >>
>  >>
>  >>
>  >>     is the time to add my
>  perspective, backing up that of
>  >>
>  >>
>  >>
>  >>     Ken.
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     Phylogenetic classification
>  is artificial. Artificial
>  >>
>  >>
>  >>
>  >>     classifications
>  >>
>  >>
>  >>
>  >>     use one set of
>  >>
>  >>
>  >>
>  >>     > > traits to group
>  taxa, e.g., molecular
>  >>
>  >>
>  >>
>  >>     races, shared traits
>  (only).
>  >>
>  >>
>  >>
>  >>     Artificial
>  >>
>  >>
>  >>
>  >>     > > classifications
>  are repeatable, yet
>  >>
>  >>
>  >>
>  >>     repeatability is not the
>  only
>  >>
>  >>
>  >>
>  >>     requirement
>  >>
>  >>
>  >>
>  >>     of
>  >>
>  >>
>  >>
>  >>     > > science.
>  Alphabetization is
>  >>
>  >>
>  >>
>  >>     repeatable.
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Principles of
>  phylogenetic classification are
>  >>
>  >>
>  >>
>  >>     artificial. Some
>  >>
>  >>
>  >>
>  >>     principles include
>  >>
>  >>
>  >>
>  >>     > > strict monophyly
>  (so long Aves),
>  >>
>  >>
>  >>
>  >>     putting known taxa at the
>  top of a tree
>  >>
>  >>
>  >>
>  >>     of
>  >>
>  >>
>  >>
>  >>     > > relationships
>  >>
>  >>
>  >>
>  >>     ("tree-thinking") rather
>  than in the tree
>  >>
>  >>    when
>  >>
>  >>
>  >>
>  >>     known
>  >>
>  >>
>  >>
>  >>     (stem-
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     thinking), ignoring the
>  probability of extinct
>  >>
>  >>    paraphyly
>  >>
>  >>
>  >>
>  >>     that casts
>  >>
>  >>
>  >>
>  >>     doubt on
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > molecular trees,
>  ignoring the evolutionary
>  >>
>  >>    importance
>  >>
>  >>
>  >>
>  >>     of autapomorphies,
>  >>
>  >>
>  >>
>  >>     > > asserting that
>  >>
>  >>
>  >>
>  >>     only zero length branches
>  imply a surviving ancestral
>  >>
>  >>
>  >>
>  >>     taxon,
>  >>
>  >>
>  >>
>  >>     > > pretending
>  >>
>  >>
>  >>
>  >>     that a cladogram is "the
>  evidence" (when it
>  >>
>  >>    is
>  >>
>  >>
>  >>
>  >>     only some
>  >>
>  >>
>  >>
>  >>     > > evidence) and
>  >>
>  >>
>  >>
>  >>     evolutionary theory is mere
>  narrative . . . you can
>  >>
>  >>
>  >>
>  >>     probably
>  >>
>  >>
>  >>
>  >>     > > think of
>  >>
>  >>
>  >>
>  >>     more phylogenetic
>  principles of classification that do
>  >>
>  >>
>  >>
>  >>     violence
>  >>
>  >>
>  >>
>  >>     to
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     evolutionary theory
>  developed only after long struggle
>  >>
>  >>    with
>  >>
>  >>
>  >>
>  >>     artificial
>  >>
>  >>
>  >>
>  >>     > > classifiers of
>  the
>  >>
>  >>
>  >>
>  >>     past.
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     Classification by
>  phylogenetic principles is actually
>  >>
>  >>
>  >>
>  >>     quite
>  >>
>  >>
>  >>
>  >>     unprincipled, and
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > serves only to
>  preserve a modification of older
>  >>
>  >>    methods
>  >>
>  >>
>  >>
>  >>     of numerical
>  >>
>  >>
>  >>
>  >>     > > taxonomy.
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Richard
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > -------
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     Richard H. Zander
>  >>
>  >>
>  >>
>  >>     > > Missouri
>  >>
>  >>
>  >>
>  >>     Botanical Garden - 4344
>  Shaw Blvd. - St. Louis -
>  >>
>  >>    Missouri
>  >>
>  >>
>  >>
>  >>     -
>  >>
>  >>
>  >>
>  >>     63110 -
>  >>
>  >>
>  >>
>  >>     > > USA richard.zander at mobot.org
>  >>
>  >>
>  >>
>  >>     Web sites:
>  >>
>  >>
>  >>
>  >>     > > http://www.mobot.org/plantscience/bfna/bfnamenu.htm
>  >>
>  >>
>  >>
>  >>     and
>  >>
>  >>
>  >>
>  >>     > > http://www.mobot.org/plantscience/resbot/
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > -----Original
>  Message-----
>  >>
>  >>
>  >>
>  >>     > > From: Taxacom
>  [mailto:taxacom-bounces at mailman.nhm.ku.edu]
>  >>
>  >>
>  >>
>  >>     On Behalf
>  >>
>  >>
>  >>
>  >>     > > Of Nico Franz
>  >>
>  >>
>  >>
>  >>     > > Sent: Friday,
>  July 10, 2015 12:16
>  >>
>  >>
>  >>
>  >>     PM
>  >>
>  >>
>  >>
>  >>     > > To: TAXACOM
>  >>
>  >>
>  >>
>  >>     > > Subject: Re:
>  [Taxacom] New paper:
>  >>
>  >>
>  >>
>  >>     Ruggiero et al. "A Higher
>  Level
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Classification of All
>  Living Organisms"
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     Computational logic? Nico
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Reasoning over
>  taxonomic change:
>  >>
>  >>
>  >>
>  >>     > >
>  >> 
> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118
>  >> 247
>  >>
>  >>
>  >>
>  >>     > > Taxonomy - for
>  computers:
>  >>
>  >>
>  >>
>  >>     > > http://biorxiv.org/content/early/2015/07/09/022145
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > -----
>  >>
>  >>
>  >>
>  >>     > > Date: Thu, 9 Jul
>  2015
>  >>
>  >>
>  >>
>  >>     > > From: Kenneth
>  Kinman
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Hi
>  >>
>  >>
>  >>
>  >>     Stephen,
>  >>
>  >>
>  >>
>  >>     > > Logically, we
>  must
>  >>
>  >>
>  >>
>  >>     remember that [...]
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>
>     _______________________________________________
>  >>
>  >>
>  >>
>  >>     > > Taxacom Mailing
>  List
>  >>
>  >>
>  >>
>  >>     > > Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>     > > The Taxacom
>  Archive back to 1992 may
>  >>
>  >>
>  >>
>  >>     be searched at:
>  >>
>  >>
>  >>
>  >>     > > http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Celebrating
>  >>
>  >>
>  >>
>  >>     28 years of Taxacom in
>  2015.
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>
>     _______________________________________________
>  >>
>  >>
>  >>
>  >>     > > Taxacom Mailing
>  List
>  >>
>  >>
>  >>
>  >>     > > Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>     > > The Taxacom
>  Archive back to 1992 may
>  >>
>  >>
>  >>
>  >>     be searched at:
>  >>
>  >>
>  >>
>  >>     > > http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>     > >
>  >>
>  >>
>  >>
>  >>     > > Celebrating
>  >>
>  >>
>  >>
>  >>     28 years of Taxacom in
>  2015.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>
>     _______________________________________________
>  >>
>  >>
>  >>
>  >>     > Taxacom Mailing List
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>     > The Taxacom Archive
>  back to 1992 may be
>  >>
>  >>
>  >>
>  >>     searched at:
>  >>
>  >>
>  >>
>  >>     http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Celebrating 28 years
>  >>
>  >>
>  >>
>  >>     of Taxacom in 2015.
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>
>     _______________________________________________
>  >>
>  >>
>  >>
>  >>     > Taxacom Mailing List
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>     > The Taxacom Archive
>  back to 1992 may be
>  >>
>  >>
>  >>
>  >>     searched at:
>  >>
>  >>
>  >>
>  >>     http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>     >
>  >>
>  >>
>  >>
>  >>     > Celebrating 28 years
>  >>
>  >>
>  >>
>  >>     of Taxacom in 2015.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>     _______________________________________________
>  >>
>  >>
>  >>
>  >>     Taxacom Mailing List
>  >>
>  >>
>  >>
>  >>     Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>     http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>     The Taxacom Archive back to
>  1992 may be
>  >>
>  >>
>  >>
>  >>     searched at: http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>     Celebrating 28 years of
>  >>
>  >>
>  >>
>  >>     Taxacom in 2015.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  _______________________________________________
>  >>
>  >>
>  >>
>  >>    Taxacom Mailing List
>  >>
>  >>
>  >>
>  >>    Taxacom at mailman.nhm.ku.edu
>  >>
>  >>
>  >>
>  >>    http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  >>
>  >>
>  >>
>  >>    The Taxacom Archive back to 1992 may
>  be searched at:
>  >> http://taxacom.markmail.org
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>    Celebrating 28 years of Taxacom in
>  2015.
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>    --
>  >>
>  >>    Richard Jensen, Professor
>  >>
>  >>    Department of Biology
>  >>
>  >>    Saint Mary's College
>  >>
>  >>    Notre Dame, IN 46556
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>   --
>  >>   Richard Jensen, Professor
>  >>   Department of Biology
>  >>   Saint Mary's College
>  >>   Notre Dame, IN 46556
>  >>
>  >>
>  > _______________________________________________
>  > Taxacom Mailing List
>  > Taxacom at mailman.nhm.ku.edu
>  > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  > The Taxacom Archive back to 1992 may be searched at:
>  > http://taxacom.markmail.org
>  >
>  > Celebrating 28 years of Taxacom in 2015.
>
>
>  --
>  Pierre DELEPORTE
>  UMR6552 EthoS
>  Université Rennes 1
>  CNRS
>  Station Biologique
>  35380 PAIMPONT
>  tél (+33) 02 99 61 81 63
>  fax (+33) 02 99 61 81 88
>
>  _______________________________________________
>  Taxacom Mailing List
>  Taxacom at mailman.nhm.ku.edu
>  http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
>  Celebrating 28 years of Taxacom in 2015.
>
>  _______________________________________________
>  Taxacom Mailing List
>  Taxacom at mailman.nhm.ku.edu
>  http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
>  Celebrating 28 years of Taxacom in 2015.
>
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
> Celebrating 28 years of Taxacom in 2015.
>



--
Richard Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
_______________________________________________
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The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org

Celebrating 28 years of Taxacom in 2015.


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